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239 results on '"Boldini, D."'

6. Effectiveness of molecular fingerprints for exploring the chemical space of natural products

Author

Boldini, D, Ballabio, D, Consonni, V, Todeschini, R, Grisoni, F, Sieber, S, Boldini, D., Ballabio, D., Consonni, V., Sieber, S. A., Boldini, D, Ballabio, D, Consonni, V, Todeschini, R, Grisoni, F, Sieber, S, Boldini, D., Ballabio, D., Consonni, V., and Sieber, S. A.

Abstract

Natural products are a diverse class of compounds with promising biological properties, such as high potency and excellent selectivity. However, they have different structural motifs than typical drug-like compounds, e.g., a wider range of molecular weight, multiple stereocenters and higher fraction of sp3-hybridized carbons. This makes the encoding of natural products via molecular fingerprints difficult, thus restricting their use in cheminformatics studies. To tackle this issue, we explored over 30 years of research to systematically evaluate which molecular fingerprint provides the best performance on the natural product chemical space. We considered 20 molecular fingerprints from four different sources, which we then benchmarked on over 100,000 unique natural products from the COCONUT (COlleCtion of Open Natural prodUcTs) and CMNPD (Comprehensive Marine Natural Products Database) databases. Our analysis focused on the correlation between different fingerprints and their classification performance on 12 bioactivity prediction datasets. Our results show that different encodings can provide fundamentally different views of the natural product chemical space, leading to substantial differences in pairwise similarity and performance. While Extended Connectivity Fingerprints are the de-facto option to encoding drug-like compounds, other fingerprints resulted to match or outperform them for bioactivity prediction of natural products. These results highlight the need to evaluate multiple fingerprinting algorithms for optimal performance and suggest new areas of research. Finally, we provide an open-source Python package for computing all molecular fingerprints considered in the study, as well as data and scripts necessary to reproduce the results, at https://github.com/dahvida/NP_Fingerprints.

Published
2024

10. A New Methodology for the Rock-Burst Assessment During Tunnel Construction

Author

Voza, A., Valguarnera, L., Fuoco, S., Ascari, G., Boldini, D., Buttafoco, D., di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Calvetti, Francesco, editor, Cotecchia, Federica, editor, Galli, Andrea, editor, and Jommi, Cristina, editor

Published
2020
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11. Computational methods

Author

di Prisco, C., primary, Boldini, D., additional, Desideri, A., additional, Bilotta, E., additional, Russo, G., additional, Callari, C., additional, Flessati, L., additional, Graziani, A., additional, and Meda, A., additional

Published
2022
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12. Assessment of excavation-related hazards and design of mitigation measures

Author

di Prisco, C., primary, Callari, C., additional, Barbero, M., additional, Bilotta, E., additional, Russo, G., additional, Boldini, D., additional, Desideri, A., additional, Flessati, L., additional, Graziani, A., additional, Luciani, A., additional, Meda, A., additional, Pescara, M., additional, Plizzari, G., additional, Tiberti, G., additional, and Sciotti, A., additional

Published
2022
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13. Input data: geotechnics

Author

Bilotta, E., primary, Boldini, D., additional, Barbero, M., additional, Martinelli, D., additional, Graziani, A., additional, and Sciotti, A., additional

Published
2022
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15. International benchmark on numerical simulations for 1D, nonlinear site response (Prenolin): Verification phase based on canonical cases

Author

Régnier, J, Bonilla, LF, Bard, PY, Bertrand, E, Hollender, F, Kawase, H, Sicilia, D, Arduino, P, Amorosi, A, Asimaki, D, Boldini, D, Chen, L, Chiaradonna, A, Demartin, F, Ebrille, M, Elgamal, A, Falcone, G, Foerster, E, Foti, S, Garini, E, Gazetas, G, Gélis, C, Ghofrani, A, Giannakou, A, Gingery, JR, Glinsky, N, Harmon, J, Hashash, Y, Iai, S, Jeremić, B, Kramer, S, Kontoe, S, Kristek, J, Lanzo, G, Di Lernia, A, Lopez-Caballero, F, Marot, M, McAllister, G, Mercerat, ED, Moczo, P, Montoya-Noguera, S, Musgrove, M, Nieto-Ferro, A, Pagliaroli, A, Pisanò, F, Richterova, A, Sajana, S, Santisi D’avila, MP, Shi, J, Silvestri, F, Taiebat, M, Tropeano, G, Verrucci, L, and Watanabe, K

Subjects
Geochemistry & Geophysics, Geophysics, Civil Engineering
Abstract

PREdiction of NOn-LINear soil behavior (PRENOLIN) is an international benchmark aiming to test multiple numerical simulation codes that are capable of predicting nonlinear seismic site response with various constitutive models. One of the objectives of this project is the assessment of the uncertainties associated with nonlinear simulation of 1D site effects. A first verification phase (i.e., comparison between numerical codes on simple idealistic cases) will be followed by a validation phase, comparing the predictions of such numerical estimations with actual strongmotion recordings obtained at well-known sites. The benchmark presently involves 21 teams and 23 different computational codes. We present here the main results of the verification phase dealing with simple cases. Three different idealized soil profiles were tested over a wide range of shear strains with different input motions and different boundary conditions at the sediment/bedrock interface. A first iteration focusing on the elastic and viscoelastic cases was proved to be useful to ensure a common understanding and to identify numerical issues before pursuing the nonlinear modeling. Besides minor mistakes in the implementation of input parameters and output units, the initial discrepancies between the numerical results can be attributed to (1) different understanding of the expression “input motion” in different communities, and (2) different implementations of material damping and possible numerical energy dissipation. The second round of computations thus allowed a convergence of all teams to the Haskell–Thomson analytical solution in elastic and viscoelastic cases. For nonlinear computations, we investigate the epistemic uncertainties related only to wave propagation modeling using different nonlinear constitutive models. Such epistemic uncertainties are shown to increase with the strain level and to reach values around 0.2 (log10 scale) for a peak ground acceleration of 5 m=s2 at the base of the soil column, which may be reduced by almost 50% when the various constitutive models used the same shear strength and damping implementation.

Published
2016

24. Rock Slope Instabilities Affecting the AlUla Archaeological Sites (KSA)

Author

Irasema Alcántara-Ayala, Željko Arbanas, David Huntley, Kazuo Konagai, Snježana Mihalić Arbanas, Matjaž Mikoš, Maneesha V. Ramesh, Kyoji Sassa, Shinji Sassa, Huiming Tang, Binod Tiwari, Gallego, J, Margottini, C, Perissé Valero, I, Spizzichino, D, Beni, T, Boldini, D, Bonometti, F, Casagli, N, Castellanza, R, Crosta, G, Frattini, P, Frodella, W, Gigli, G, Lusini, E, Rigamonti, S, Rusconi, G, Vitrano, L, Gallego, José Ignacio, Margottini, Claudio, Perissé Valero, Ingrid, Spizzichino, Daniele, Beni, Tommaso, Boldini, Daniela, Bonometti, Francesca, Casagli, Nicola, Castellanza, Riccardo, Crosta, Giovanni Battista, Frattini, Paolo, Frodella, William, Gigli, Giovanni, Lusini, Edoardo, Rigamonti, Serena, Rusconi, Giulia, Vitrano, Lorenzo, Irasema Alcántara-Ayala, Željko Arbanas, David Huntley, Kazuo Konagai, Snježana Mihalić Arbanas, Matjaž Mikoš, Maneesha V. Ramesh, Kyoji Sassa, Shinji Sassa, Huiming Tang, Binod Tiwari, Gallego, J, Margottini, C, Perissé Valero, I, Spizzichino, D, Beni, T, Boldini, D, Bonometti, F, Casagli, N, Castellanza, R, Crosta, G, Frattini, P, Frodella, W, Gigli, G, Lusini, E, Rigamonti, S, Rusconi, G, Vitrano, L, Gallego, José Ignacio, Margottini, Claudio, Perissé Valero, Ingrid, Spizzichino, Daniele, Beni, Tommaso, Boldini, Daniela, Bonometti, Francesca, Casagli, Nicola, Castellanza, Riccardo, Crosta, Giovanni Battista, Frattini, Paolo, Frodella, William, Gigli, Giovanni, Lusini, Edoardo, Rigamonti, Serena, Rusconi, Giulia, and Vitrano, Lorenzo

Abstract

The paper focuses on the geomorphological processes and potential geo-hazards affecting the cultural heritage rock-cut sites of AlUla region. Its best-known site is Hegra, with more than 110 monumental tombs with elaborated façades carved directly into the sandstone rock. In addition, AlUla hosts a number of fascinating historical and archaeological sites such as its Old Town, surrounded by an ancient oasis, and Dadan, the capital of the Dadan and Lihyan kingdoms. The study is mainly aimed at investigating the local rock material, evaluating characteristics of rock masses, understanding rock degradation processes and characterizing the potential impact of slope instabilities on the conservation of cultural heritage.

Published
2023

32. Computational methods

Author

di Prisco C., Boldini D., Desideri A., Bilotta E., Russo G., Callari C., Flessati L., Graziani A., Meda A., di Prisco, C., Boldini, D., Desideri, A., Bilotta, E., Russo, G., Callari, C., Flessati, L., Graziani, A., and Meda, A.

Subjects
FEM, modelling approaches, FDM, DEM, limit equilibrium method, limit analysis
Abstract

This chapter is dedicated to the presentation of the most popular methods of analysis employed to solve geotechnical boundary value problems, with special emphasis on the assessment of the potential hazards related to tunnelling. In particular, in Section 9.1, the general framework is outlined with reference to numerical solutions of coupled hydro-thermo-chemo-mechanical boundary value problems. In Section 9.2, the excavation phase is considered by analysing the response of the soil/rock mass close to the tunnel (‘near field’), whereas in Section 9.3, far-field tunnelling-induced modifications in stress and deformation fields and, if relevant, in the pore pressure distribution during the construction are considered. These analyses are instrumental in the assessment of the tunnel stability and in the design of the primary and final linings. Specific emphasis is given to some particularly demanding situations for tunnel construction and performance (i.e. rock burst phenomena, swelling or squeezing behaviour of the rock mass, etc.) requiring non-standard approaches to be implemented. Lastly, in Section 9.4, long-term system response is analysed. The accent is put on: (i) delayed/evolving with time strain and stress distributions (viscous and hydro-chemical effects, Section 9.4.1–9.4.3), (ii) seismic perturbations, (iii) gravitational and tectonic movements (landslides and faults) and (iv) thermal loading (fire in tunnel).

Published
2022

33. Assessment of excavation-related hazards and design of mitigation measures

Author

di Prisco, C., Callari, C., Barbero, M., Bilotta, E., Russo, G., Boldini, D., Desideri, A., Flessati, L., Graziani, A., Luciani, A., Meda, A., Pescara, M., Plizzari, G., Tiberti, G., Sciotti, A., di Prisco, C., Callari, C., Barbero, M., Bilotta, E., Russo, G., Boldini, D., Desideri, A., Flessati, L., Graziani, A., Luciani, A., Meda, A., Pescara, M., Plizzari, G., Tiberti, G., and Sciotti, A.

Subjects
tunnelling, design principles, tunnel, tunnelling, tunnel, design principles
Abstract

This chapter is devoted to the presentation of the most popular approaches employed to design mitigation measures. Initially, the mitigation measures necessary for a safe excavation and a permanent cavity stabilization are considered. Subsequently, the observational method, a design procedure aimed at optimizing the management of the unavoidable geological and geotechnical uncertainties affecting both tunnel design and construction, is presented. Finally, the long-term tunnel performance under accidental loads is discussed.

Published
2022

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